Precomputed images set up from tiff file

[ming yan]

Hi all:

I'm new to Neuroglancer and I recently had it run locally in the Docker container (localhost). I want to visualize a small .tiff file (stored locally) in Nueroglancer just to get some feel of it, but I'm confused about how to properly generate the precomputed format, to my understanding, it should be a URL that we specify in the <source> tab in Neuroglancer. Can someone shed some light? 

Thank you very much.

Ming

[Ecks Gee]

I don't believe neuroglancer can consume TIFF directly.

We have always converted the said TIFF to precomputed format with neuroglacer-scripts and served it separately.

Perhaps There is a more direct way of visualising it by first converting it to an numpy array, then with the neuroglancer 's python part?

[ming yan]

Thanks for your reply Ecks! 

I ran into some problems when trying to visualize NIFTI file in neuroglancer, does anyone know how to fix it? 

I'm trying the colin27T1_seg.nii.gz file, which is one of the examples of neuroglancer-scripts. I have neuroglancer running on my localhost and followed the steps in "Conversion of the grey-level template image (MNI Colin27 T1 MRI)" documentation, and got the files & directories already including 1mm, 2mm, info, info_fullres.json, transform.json. But when I load it in neuroglancer, It seems like the image layer is not being visualized, Can someone provide some guidance?

Thanks a lot! 

[ming yan]

Hi Guys: 

I have a question about CloudVolume and visualizing in Neuroglancer. 

I'm using a tiff stack ~14GB, and run neuroglancer in a docker container on my local machine. I used CloudVolume to chunk the volumes since neuroglancer-scripts got killed due to a shortage of space. 

So far I've created the info file and different chunks of pre-computed data, but in neuroglancer nothing is being visualized. Can anyone shed some light on this? 

The attached pics are (from left to right): info file, samples of chunks created, and my view in neuroglancer. 

Thank you very much!

Ming

      

[XG]

You might also want to cross post this in CloudVolume GitHub issue. Developers tend to monitor their GitHub issues a lot more

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[ming yan]

Just posted there, thanks Ecks!